Because node markers could be over any colour (even the default colour for markers) a trick to keep them visible at all times is to calculate what the inverse of the colour under the node marker is and make the node market the inverse of that colour, to provide a high-contrast marker no matter what the colour under it is. 

Unfortunately, when two markers are atop each other, they are both set to be the inverse of the colour under it, the effect is that the cancel eachother out, and thus disappear instead of standing out. 

Walking through and example:

Let's say the bottom colour is yellow, the node marker over it would be inverted into purplish colour. This is the desired effect, because we can easily see the node in contrast to the yellow object underneath.

Now if there's another node on top of that:

The node on top of that takes the inverse of the purple colour node under it, and turns it back to yellow (the inverse of purple), and thus it looks like the markers have vanished. They haven't actually vanished, it's just that the top node turned it's colour to the same colour as the yellow under both nodes (the inverse of the inverse of yellow is yellow).

So what we really want is for the nodes to ignore the colour of other nodes under them, so if they are stacked, it only takes into account the colour of non-node objects to perform the inverse. Additionally, it would be handy to have, at the center of each node marker a single pixel-width dot representing the true center of the node marker. This way, even though the nodes would be the same colour, you still have a chance of distinguishing that there are 2 nodes atop each other... or you can just zoom in enough to where they don't overlap, of course. :)

-C